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Yu FCY, Vallejo JLG, Barca GMJ. Automatic molecular fragmentation by evolutionary optimisation. J Cheminform 2024; 16:102. [PMID: 39160576 PMCID: PMC11331744 DOI: 10.1186/s13321-024-00896-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Molecular fragmentation is an effective suite of approaches to reduce the formal computational complexity of quantum chemistry calculations while enhancing their algorithmic parallelisability. However, the practical applicability of fragmentation techniques remains hindered by a dearth of automation and effective metrics to assess the quality of a fragmentation scheme. In this article, we present the Quick Fragmentation via Automated Genetic Search (QFRAGS), a novel automated fragmentation algorithm that uses a genetic optimisation procedure to generate molecular fragments that yield low energy errors when adopted in Many Body Expansions (MBEs). Benchmark testing of QFRAGS on protein systems with less than 500 atoms, using two-body (MBE2) and three-body (MBE3) MBE calculations at the HF/6-31G* level, reveals mean absolute energy errors (MAEE) of 20.6 and 2.2 kJ mol - 1 , respectively. For larger protein systems exceeding 500 atoms, MAEEs are 181.5 kJ mol - 1 for MBE2 and 24.3 kJ mol - 1 for MBE3. Furthermore, when compared to three manual fragmentation schemes on a 40-protein dataset, using both MBE and Fragment Molecular Orbital techniques, QFRAGS achieves comparable or often lower MAEEs. When applied to a 10-lipoglycan/glycolipid dataset, MAEs of 7.9 and 0.3 kJ mol - 1 were observed at the MBE2 and MBE3 levels, respectively.Scientific Contribution This Article presents the Quick Fragmentation via Automated Genetic Search (QFRAGS), an innovative molecular fragmentation algorithm that significantly improves upon existing molecular fragmentation approaches by specifically addressing their lack of automation and effective fragmentation quality metrics. With an evolutionary optimisation strategy, QFRAGS actively pursues high quality fragments, generating fragmentation schemes that exhibit minimal energy errors on systems with hundreds to thousands of atoms. The advent of QFRAGS represents a significant advancement in molecular fragmentation, greatly improving the accessibility and computational feasibility of accurate quantum chemistry calculations.
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Affiliation(s)
- Fiona C Y Yu
- School of Computing, Australian National University, Canberra, 2601, ACT, Australia
| | | | - Giuseppe M J Barca
- School of Computing and Information Technology, The University of Melbourne, Melbourne, 3052, VIC, Australia.
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Kokuszi LTF, Paes YM, Faria ALS, Alvarado-Huayhuaz J, Balboni MDC, Dos Santos MC, Dos Santos SC, de Menezes Vicenti JR, Parize AL, Werhli AV, Dos Santos Machado K, de Lima VR. Benzohydroxamate and nitrobenzohydroxamate affect membrane order: Correlations between spectroscopic and molecular dynamics to approach tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184378. [PMID: 39163923 DOI: 10.1016/j.bbamem.2024.184378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/17/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024]
Abstract
This work correlates the effects of benzohydroxamate (BH) and nitrobenzohydroxamate (NBH) anions in two membrane models which may be used for anti-tuberculosis (anti-TB) spectroscopic studies and/or computational studies. Firstly, the BH and NBH influence in the physico-chemical properties of soy asolectin (ASO)-based large multilamellar vesicles (MLVs) were evaluated by spectroscopic and calorimetric studies. In parallel, the BH and NBH interaction with a Mycobacterium tuberculosis (Mtb) inner membrane model, composed of phosphatidyl-myo-inositol-dimannoside (PIM2), was investigated by molecular dynamics (MD) simulations. Spectroscopic data showed a localization of BH close to the lipid phosphate group, while NBH was found close to the choline region. The BH ordered the ASO choline, phosphate and carbonyl regions and disrupted the acyl methylenes, reducing the membrane packing of the lipid hydrophobic region. On the other hand, NBH showed an ordering effect in all the lipid groups (polar, interface and hydrophobic ones). By MD studies, it was found that NBH enhanced the stability of the PIM2 membrane more than BH, while also being positioned closer to its mannosyl oxygens. As in ASO MLVs, BH was localized close to the PIM2 phosphate group and disrupted its acyl chains. However, higher values of lateral diffusion were observed for NBH than BH. Despite this, BH and NBH increased the membrane thickness by 35 %, which suggests a global ordering effect of both drugs. Findings of this work reinforce the accordance and complementarity between MLVs based on ASO and the PIM2 MD model results to study the drug effects in Mtb membrane properties.
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Affiliation(s)
- Lucas Thadeu Felipe Kokuszi
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil
| | - Yago Mendes Paes
- COMBI-Lab, Grupo de Biologia Computacional, Centro de Ciências Computacionais, Universidade Federal do Rio Grande, Av. Itália, km 8, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil
| | - Aline Loise Santana Faria
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil
| | - Jesus Alvarado-Huayhuaz
- COMBI-Lab, Grupo de Biologia Computacional, Centro de Ciências Computacionais, Universidade Federal do Rio Grande, Av. Itália, km 8, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil
| | - Maurício Dornelles Caldeira Balboni
- COMBI-Lab, Grupo de Biologia Computacional, Centro de Ciências Computacionais, Universidade Federal do Rio Grande, Av. Itália, km 8, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil
| | - Marinalva Cardoso Dos Santos
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil
| | - Sandra Cruz Dos Santos
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil
| | - Juliano Rosa de Menezes Vicenti
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil
| | - Alexandre Luis Parize
- Programa de Pós-Graduação em Química-PPGQ, Departamento de Química, Centro de Ciências Físicas e Matemáticas-CFM, Universidade Federal de Santa Catarina-UFSC, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC 88040-900, Brazil
| | - Adriano Velasque Werhli
- COMBI-Lab, Grupo de Biologia Computacional, Centro de Ciências Computacionais, Universidade Federal do Rio Grande, Av. Itália, km 8, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil
| | - Karina Dos Santos Machado
- COMBI-Lab, Grupo de Biologia Computacional, Centro de Ciências Computacionais, Universidade Federal do Rio Grande, Av. Itália, km 8, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil.
| | - Vânia Rodrigues de Lima
- Grupo de Investigação em Interações Moleculares em Membranas, Programa de Pós-Graduação em Química Tecnológica e Ambiental (PPGQTA), Escola de Química e Alimentos (EQA), 96203-900 Rio Grande, RS, Brazil.
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Islam S, Shibly AZ. Exploring Bryophyllum pinnatum compounds as potential inhibitors for Vespula vulgaris allergen proteins: A systematic computational approach. Heliyon 2024; 10:e34713. [PMID: 39170106 PMCID: PMC11336329 DOI: 10.1016/j.heliyon.2024.e34713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/23/2024] Open
Abstract
Vespula vulgaris (V. vulgaris), commonly known as the common wasp, poses a significant health threat due to its venom-induced allergic reactions. This research focused on the exploration of bioactive compounds from Bryophyllum pinnatum as potential inhibitors for V. vulgaris allergen proteins, including Phospholipase A1 (Ves V1), Hyaluronoglucosaminidase (Ves V2), and Antigen 5 (Ves V5). Through a multidisciplinary approach involving literature reviews, molecular docking analyses, ADMET assessments and Molecular Dynamics Simulations (MDS) of 100ns we identified two promising drug candidates from four bioactive compounds- Bryophyllin A, Bryophyllin B, Bryotoxin A, and Bryotoxin B of Bryophyllum pinnatum. Molecular docking results revealed strong binding interactions, with Bryophyllin B and Bryotoxin A consistently exhibiting the highest affinity (-9.6 kcal/mol and -10.0 kcal/mol) across the allergen proteins. ADMET analyses highlighted Bryophyllin B as a favorable candidate, showing high absorption (HIA: 92.1 %), minimal metabolic interactions (CYP1A2: No), and a low toxicity profile (LD50 (rat): 2.431). MDS analysis revealed Bryophyllin B and Bryotoxin A as promising drug inhibitors, exhibiting the highest binding stability with the allergen proteins of V. vulgaris, as indicated by the lowest Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (RG) values and highest protein-ligand contacts. Our study provides valuable insights into the therapeutic potential of Bryophyllum pinnatum compounds as inhibitors for V. vulgaris allergen proteins having two promising candidates- Bryophyllin B and Bryotoxin A.
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Affiliation(s)
- Sirajul Islam
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Santosh, 1902, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Santosh, 1902, Bangladesh
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Reghunandanan K, T P A, Krishnan N, K M D, Prasad R, Nelson-Sathi S, Chandramohanadas R. Search for novel Plasmodium falciparum PfATP4 inhibitors from the MMV Pandemic Response Box through a virtual screening approach. J Biomol Struct Dyn 2024; 42:6200-6211. [PMID: 37424150 DOI: 10.1080/07391102.2023.2232459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
Owing to its life cycle involving multiple hosts and species-specific biological complexities, a vaccine against Plasmodium, the causative agent of Malaria remains elusive. This makes chemotherapy the only viable means to address the clinical manifestations and spread of this deadly disease. However, rapid surge in antimalarial resistance poses significant challenges to our efforts to eliminate Malaria since the best drug available to-date; Artemisinin and its combinations are also rapidly losing efficacy. Sodium ATPase (PfATP4) of Plasmodium has been recently explored as a suitable target for new antimalarials such as Cipargamin. Prior studies showed that multiple compounds from the Medicines for Malaria Venture (MMV) chemical libraries were efficient PfATP4 inhibitors. In this context, we undertook a structure- based virtual screening approach combined to Molecular Dynamic (MD) simulations to evaluate whether new molecules with binding affinity towards PfATP4 could be identified from the Pandemic Response Box (PRB), a 400-compound library of small molecules launched in 2019 by MMV. Our analysis identified new molecules from the PRB library that showed affinity for distinct binding sites including the previously known G358 site, several of which are clinically used anti-bacterial (MMV1634383, MMV1634402), antiviral (MMV010036, MMV394033) or antifungal (MMV1634494) agents. Therefore, this study highlights the possibility of exploiting PRB molecules against Malaria through abrogation of PfATP4 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Keerthy Reghunandanan
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Akhila T P
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nandini Krishnan
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Darsana K M
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Roshny Prasad
- DBT-Rajiv Gandhi Centre for Biotechnology, Bioinformatics Laboratory, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- DBT-Rajiv Gandhi Centre for Biotechnology, Bioinformatics Laboratory, Thiruvananthapuram, India
| | - Rajesh Chandramohanadas
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
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Islam S, Amin MA, Rengasamy KR, Mohiuddin AKM, Mahmud S. Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach. Cancer Med 2024; 13:e70074. [PMID: 39101505 PMCID: PMC11299079 DOI: 10.1002/cam4.70074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Breast cancer, a leading cause of female mortality, is closely linked to mutations in estrogen receptor beta (ESR2), particularly in the ligand-binding domain, which contributed to altered signaling pathways and uncontrolled cell growth. OBJECTIVES/AIMS This study investigates the molecular and structural aspects of ESR2 mutant proteins to identify shared pharmacophoric regions of ESR2 mutant proteins and potential therapeutic targets aligned within the pharmacophore model. METHODS This study was initiated by establishing a common pharmacophore model among three mutant ESR2 proteins (PDB ID: 2FSZ, 7XVZ, and 7XWR). The generated shared feature pharmacophore (SFP) includes four primary binding interactions: Hydrogen bond donors (HBD), hydrogen bond acceptors (HBA), hydrophobic interactions (HPho), and Aromatic interactions (Ar), along with halogen bond donors (XBD) and totalling 11 features (HBD: 2, HBA: 3, HPho: 3, Ar: 2, XBD: 1). By employing an in-house Python script, these 11 features distributed into 336 combinations, which were used as query to isolate a drug library of 41,248 compounds and subjected to virtual screening through the generated SFP. RESULTS The virtual screening demonstrated 33 hits showing potential pharmacophoric fit scores and low RMSD value. The top four compounds: ZINC94272748, ZINC79046938, ZINC05925939, and ZINC59928516 showed a fit score of more than 86% and satisfied the Lipinski rule of five. These four compounds and a control underwent molecular (XP Glide mode) docking analysis against wild-type ESR2 protein (PDB ID: 1QKM), resulting in binding affinity of -8.26, -5.73, -10.80, and -8.42 kcal/mol, respectively, along with the control -7.2 kcal/mol. Furthermore, the stability of the selected candidates was determined through molecular dynamics (MD) simulations of 200 ns and MM-GBSA analysis. CONCLUSION Based on MD simulations and MM-GBSA analysis, our study identified ZINC05925939 as a promising ESR2 inhibitor among the top four hits. However, it is essential to conduct further wet lab evaluation to assess its efficacy.
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Affiliation(s)
- Sirajul Islam
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Kannan R.R. Rengasamy
- Laboratory of Natural Products and Medicinal Chemistry (LNPMC), Center for Global Health Research, Saveetha Medical College and HospitalSaveetha Institute of Medical and Technical Sciences (SIMATS)ThandalamChennai602105India
| | - A. K. M. Mohiuddin
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
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Brueckner AC, Shields B, Kirubakaran P, Suponya A, Panda M, Posy SL, Johnson S, Lakkaraju SK. MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. J Comput Aided Mol Des 2024; 38:24. [PMID: 39014286 DOI: 10.1007/s10822-024-00564-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein-ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein-ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein-ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure-activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9.
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Affiliation(s)
| | - Benjamin Shields
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Palani Kirubakaran
- Biocon Bristol Myers Squibb R&D Centre, Bangalore, 560099, Karnataka, India
| | - Alexander Suponya
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Manoranjan Panda
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Shana L Posy
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Stephen Johnson
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
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Binder J, Winkeljann J, Steinegger K, Trnovec L, Orekhova D, Zähringer J, Hörner A, Fell V, Tinnefeld P, Winkeljann B, Frieß W, Merkel OM. Closing the Gap between Experiment and Simulation─A Holistic Study on the Complexation of Small Interfering RNAs with Polyethylenimine. Mol Pharm 2024; 21:2163-2175. [PMID: 38373164 DOI: 10.1021/acs.molpharmaceut.3c00747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Rational design is pivotal in the modern development of nucleic acid nanocarrier systems. With the rising prominence of polymeric materials as alternatives to lipid-based carriers, understanding their structure-function relationships becomes paramount. Here, we introduce a newly developed coarse-grained model of polyethylenimine (PEI) based on the Martini 3 force field. This model facilitates molecular dynamics simulations of true-sized PEI molecules, exemplified by molecules with molecular weights of 1.3, 5, 10, and 25 kDa, with degrees of branching between 50.0 and 61.5%. We employed this model to investigate the thermodynamics of small interfering RNA (siRNA) complexation with PEI. Our simulations underscore the pivotal role of electrostatic interactions in the complexation process. Thermodynamic analyses revealed a stronger binding affinity with increased protonation, notably in acidic (endosomal) pH, compared to neutral conditions. Furthermore, the molecular weight of PEI was found to be a critical determinant of binding dynamics: smaller PEI molecules closely enveloped the siRNA, whereas larger ones extended outward, facilitating the formation of complexes with multiple RNA molecules. Experimental validations, encompassing isothermal titration calorimetry and single-molecule fluorescence spectroscopy, aligned well with our computational predictions. Our findings not only validate the fidelity of our PEI model but also accentuate the importance of in silico data in the rational design of polymeric drug carriers. The synergy between computational predictions and experimental validations, as showcased here, signals a refined and precise approach to drug carrier design.
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Affiliation(s)
- Jonas Binder
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
| | - Joshua Winkeljann
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
- Chair of Experimental Physics I, University of Augsburg, Universitätsstraße 1, 86519 Augsburg, Germany
| | - Katharina Steinegger
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
| | - Lara Trnovec
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
| | - Daria Orekhova
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
| | - Jonas Zähringer
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
| | - Andreas Hörner
- Chair of Experimental Physics I, University of Augsburg, Universitätsstraße 1, 86519 Augsburg, Germany
| | - Valentin Fell
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
| | - Philip Tinnefeld
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
| | - Benjamin Winkeljann
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
| | - Wolfgang Frieß
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
| | - Olivia M Merkel
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus B, 81377 München, Germany
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80799 München, Germany
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Bappi MH, Mia MN, Ansari SA, Ansari IA, Prottay AAS, Akbor MS, El-Nashar HAS, El-Shazly M, Mubarak MS, Torequl Islam M. Quercetin increases the antidepressant-like effects of sclareol and antagonizes diazepam in thiopental sodium-induced sleeping mice: A possible GABAergic transmission intervention. Phytother Res 2024; 38:2198-2214. [PMID: 38414297 DOI: 10.1002/ptr.8139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/29/2024]
Abstract
Quercetin is the most common polyphenolic flavonoid present in fruits and vegetables demonstrating versatile health-promoting effects. This study aimed to examine the effects of quercetin (QR) and sclareol (SCL) on the thiopental sodium (TS)-induced sleeping and forced swimming test (FST) mouse models. SCL (1, 5, and 10 mg/kg, p.o.) or QR (50 mg/kg, p.o.) and/or diazepam (DZP) (3 mg/kg, i.p.) were employed. After 30 min of TS induction, individual or combined effects on the animals were checked. In the FST test, the animals were subjected to forced swimming after 30 min of administration of the test and/or controls for 5 min. In this case, immobility time was measured. In silico studies were conducted to evaluate the involvement of GABA receptors. SCL (5 and 10 mg/kg) significantly increased the latency and decreased sleeping time compared to the control in the TS-induced sleeping time study. DZP (3 mg/kg) showed a sedative-like effect in animals in both sleeping and FST studies. QR (50 mg/kg) exhibited a similar pattern of activity as SCL. However, its effects were more prominent than those of SCL groups. SCL (10 mg/kg) altered the DZP-3-mediated effects. SCL-10 co-treated with QR-50 significantly (p < 0.05) increased the latency and decreased sleep time and immobility time, suggesting possible synergistic antidepressant-like effects. In silico studies revealed that SCL and QR demonstrated better binding affinities with GABAA receptor, especially α2, α3, and α5 subunits. Both compounds also exhibited good ADMET and drug-like properties. In animal studies, the both compounds worked synergistically to provide antidepressant-like effects in a slightly different fashion. As a conclusion, the combined administration of SCL and QR may be used in upcoming neurological clinical trials, according to in vivo and in silico findings. However, additional investigation is necessary to verify this behavior and clarify the potential mechanism of action.
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Affiliation(s)
- Mehedi Hasan Bappi
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Nayem Mia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Irfan Aamer Ansari
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Abdullah Al Shamsh Prottay
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Showkoth Akbor
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Heba A S El-Nashar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
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Croney K, McCarty J. Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. J Phys Chem B 2024; 128:3102-3112. [PMID: 38516924 PMCID: PMC11000218 DOI: 10.1021/acs.jpcb.3c07972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The yeast cytosine deaminase (yCD) enzyme/5-fluorocytosine prodrug system is a promising candidate for targeted chemotherapeutics. After conversion of the prodrug into the toxic chemotherapeutic drug, 5-fluorouracil (5-FU), the slow product release from the enzyme limits the overall catalytic efficiency of the enzyme/prodrug system. Here, we present a computational study of the product release of the anticancer drug, 5-FU, from yCD using metadynamics. We present a comparison of the 5-FU drug to the natural enzyme product, uracil. We use volume-based metadynamics to compute the free energy landscape for product release and show a modest binding affinity for the product to the enzyme, consistent with experiments. Next, we use infrequent metadynamics to estimate the unbiased release rate from Kramers time-dependent rate theory and find a favorable comparison to experiment with a slower rate of product release for the 5-FU system. Our work demonstrates how adaptive sampling methods can be used to study the protein-ligand unbinding process for engineering enzyme/prodrug systems and gives insights into the molecular mechanism of product release for the yCD/5-FU system.
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Affiliation(s)
- Kayla
A. Croney
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
| | - James McCarty
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
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10
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Dao TNP, Onikanni SA, Fadaka AO, Klein A, Tran VD, Le MH, Wang CH, Chang HH. In silico identification of compounds from Piper sarmentosum Roxb leaf fractionated extract inhibit interleukin-6 to prevent rheumatoid arthritis. Front Pharmacol 2024; 15:1358037. [PMID: 38576490 PMCID: PMC10991700 DOI: 10.3389/fphar.2024.1358037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
Objective: Medicinal herbs with a phytonutrient background has been applied globally as major alternatives to ameliorate the continuous increase in rheumatoid arthritis cases worldwide. We herein aimed to critically examine the bioactive components of the medicinal herb Piper sarmentosum Roxb leaf fractionated extract for its potential to inhibit the influx of interleukin-6 (IL-6) in rheumatoid arthritis. Methods: The Schrödinger platform was employed as the main computational acumen for the screening of bioactive compounds identified and reference compounds subjected to molecular simulation (MDS) for analyzing the stability of docked complexes to assess fluctuations and conformational changes during protein-ligand interactions. Results: The values of the simulatory properties and principal component analysis (PCA) revealed the good stability of these phytochemicals in the active pocket of interleukin-6 (IL-6). Discussion: Our findings reveal new strategies in which these phytochemicals are potential inhibitory agents that can be modified and further evaluated to develop more effective agents for the management of rheumatoid arthritis, thereby providing a better understanding and useful model for the reproduction and/or discovery of new drugs for the management of rheumatoid arthritis and its complications.
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Affiliation(s)
- Tran Nhat Phong Dao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Faculty of Traditional Medicine, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Sunday Amos Onikanni
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Chemical Sciences, Biochemistry Unit, Afe-Babalola University, Ado-Ekiti, Nigeria
| | | | - Ashwil Klein
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Van De Tran
- Department of Health Organization and Management, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Minh Hoang Le
- Faculty of Traditional Medicine, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Chih-Hao Wang
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Cell Biology, China Medical University, Taichung, Taiwan
| | - Hen-Hong Chang
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung, Taiwan
- Department of Chinese Medicine, China Medical University Hospital, Taichung, Taiwan
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11
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Ries B, Alibay I, Swenson DWH, Baumann HM, Henry MM, Eastwood JRB, Gowers RJ. Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. J Chem Theory Comput 2024; 20:1862-1877. [PMID: 38330251 PMCID: PMC10941767 DOI: 10.1021/acs.jctc.3c01206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Relative binding free energy (RBFE) calculations have emerged as a powerful tool that supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular, the setup of such calculations. Atom mapping algorithms are an essential component in setting up automatic large-scale hybrid-topology RBFE calculation campaigns. Traditional algorithms typically employ a 2D subgraph isomorphism solver (SIS) in order to estimate the maximum common substructure. SIS-based approaches can be limited by time-intensive operations and issues with capturing geometry-linked chemical properties, potentially leading to suboptimal solutions. To overcome these limitations, we have developed Kartograf, a geometric-graph-based algorithm that uses primarily the 3D coordinates of atoms to find a mapping between two ligands. In free energy approaches, the ligand conformations are usually derived from docking or other previous modeling approaches, giving the coordinates a certain importance. By considering the spatial relationships between atoms related to the molecule coordinates, our algorithm bypasses the computationally complex subgraph matching of SIS-based approaches and reduces the problem to a much simpler bipartite graph matching problem. Moreover, Kartograf effectively circumvents typical mapping issues induced by molecule symmetry and stereoisomerism, making it a more robust approach for atom mapping from a geometric perspective. To validate our method, we calculated mappings with our novel approach using a diverse set of small molecules and used the mappings in relative hydration and binding free energy calculations. The comparison with two SIS-based algorithms showed that Kartograf offers a fast alternative approach. The code for Kartograf is freely available on GitHub (https://github.com/OpenFreeEnergy/kartograf). While developed for the OpenFE ecosystem, Kartograf can also be utilized as a standalone Python package.
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Affiliation(s)
- Benjamin Ries
- Medicinal
Chemistry, Boehringer Ingelheim Pharma GmbH
& Co KG, Birkendorfer Str 65, 88397 Biberach an der Riss, Germany
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
| | - Irfan Alibay
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
| | - David W. H. Swenson
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
| | - Hannah M. Baumann
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
| | - Michael M. Henry
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
- Computational
and Systems Biology Program, Sloan Kettering
Institute, Memorial Sloan Kettering Cancer Center, New York, 1275 New York, United States
| | - James R. B. Eastwood
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
| | - Richard J. Gowers
- Open
Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
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12
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Zhang DT, Baldauf L, Roet S, Lervik A, van Erp TS. Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps. Proc Natl Acad Sci U S A 2024; 121:e2318731121. [PMID: 38315841 PMCID: PMC10873605 DOI: 10.1073/pnas.2318731121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue without altering the potential energy landscape or dynamics, enabling recovery of both thermodynamic and kinetic information. However, despite its exponential acceleration compared to standard molecular dynamics, generating numerous trajectories can still require a long time. By harnessing our recent algorithmic innovations-particularly subtrajectory moves with high acceptance, coupled with asynchronous replica exchange featuring infinite swaps-we establish a highly parallelizable and rapidly converging path sampling protocol, compatible with diverse high-performance computing architectures. We demonstrate our approach on the liquid-vapor phase transition in superheated water, the unfolding of the chignolin protein, and water dissociation. The latter, performed at the ab initio level, achieves comparable statistical accuracy within days, in contrast to a previous study requiring over a year.
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Affiliation(s)
- Daniel T. Zhang
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Lukas Baldauf
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Sander Roet
- Department of Chemistry, Utrecht University, Utrecht3584 CH, Netherlands
| | - Anders Lervik
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
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13
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Markey C, Croset S, Woolley OR, Buldun CM, Koch C, Koller D, Reker D. Characterizing emerging companies in computational drug development. NATURE COMPUTATIONAL SCIENCE 2024; 4:96-103. [PMID: 38413778 DOI: 10.1038/s43588-024-00594-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
Computation promises to accelerate, de-risk and optimize drug research and development. An increasing number of companies have entered this space, specializing in the design of new algorithms, computing on proprietary data, and/or development of hardware to improve distinct drug pipeline stages. The large number of such companies and their unique strategies and deals have created a highly complex and competitive industry. We comprehensively analyze the companies in this space to highlight trends and opportunities, identifying highly occupied areas of risk and currently underrepresented niches of high value.
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Affiliation(s)
- Chloe Markey
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | | | | | | | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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14
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Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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15
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Menchon G, Maveyraud L, Czaplicki G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol 2024; 2714:33-83. [PMID: 37676592 DOI: 10.1007/978-1-0716-3441-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).
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Affiliation(s)
- Grégory Menchon
- Inserm U1242, Oncogenesis, Stress and Signaling (OSS), Université de Rennes 1, Rennes, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Georges Czaplicki
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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16
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Das D, Mallick B, Sinha S, Ganguli S, Samanta D, Banerjee R, Roy D. Unearthing the inhibitory potential of phytochemicals from Lawsonia inermis L. and some drugs against dengue virus protein NS1: an in silico approach. J Biomol Struct Dyn 2023:1-18. [PMID: 38157248 DOI: 10.1080/07391102.2023.2298730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Dengue has received the status of an epidemic and endemic disease, with countless number of infections every year. Due to the unreliability of vaccines and non-specificity of drugs, it becomes necessary to find plant-based alternatives, with less harmful side effects. Lawsonia inermis L., is the sole source of dye, Mehendi. The rich repertoire of phytochemicals makes it useful, medicinally. The main objectives of the study are to explore the anti-dengue properties of the phytochemicals from Lawsonia inermis, and to shortlist potential candidates in curing the disease. Phytochemicals from the plant, and a set of drugs were screened and docked against NS1 protein, a less explored drug target, needed for maintenance of virus life cycle. Ligand screening and docking analysis concluded gallic acid, and chlorogenic acid to be good candidates, exhibiting high binding affinity and extensive interactions with the protein. From among the shortlisted drugs, only Vibegron showed effective binding affinity with NS1 protein with zero violations to the Lipinski's Rule of 5. Molecular dynamic simulations, executed for a time period of 100 nanoseconds, reveal the performance of a ligand within a solvated system. Chlorogenic and gallic acid, formed more stable and compact complexes with protein, with stable energy parameters and strong binding affinity. This was further validated with snapshots taken every 50 nanoseconds, showing no change in binding site between the ligand and protein, within the stipulated time frame. It was interesting to see that, a phenol (chlorogenic acid), served as a better drug candidate, against the NS1 protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debapriya Das
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Bidisha Mallick
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Suchita Sinha
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Sayak Ganguli
- Post Graduate Department of Biotechnology, St. Xaviers' College (Autonomous), Kolkata, India
| | - Dipu Samanta
- Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, India
| | - Rajat Banerjee
- Dr. BC Chandra Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Debleena Roy
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
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17
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Kazi JU, Al Ashiri L, Purohit R, Rönnstrand L. Understanding the Role of Activation Loop Mutants in Drug Efficacy for FLT3-ITD. Cancers (Basel) 2023; 15:5426. [PMID: 38001685 PMCID: PMC10670458 DOI: 10.3390/cancers15225426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The type III receptor tyrosine kinase FLT3 is a pivotal kinase for hematopoietic progenitor cell regulation, with significant implications in acute myeloid leukemia (AML) through mutations like internal tandem duplication (ITD). This study delves into the structural intricacies of FLT3, the roles of activation loop mutants, and their interaction with tyrosine kinase inhibitors. Coupled with this, the research leverages molecular contrastive learning and protein language modeling to examine interactions between small molecule inhibitors and FLT3 activation loop mutants. Utilizing the ConPLex platform, over 5.7 million unique FLT3 activation loop mutants-small molecule pairs were analyzed. The binding free energies of three inhibitors were assessed, and cellular apoptotic responses were evaluated under drug treatments. Notably, the introduction of the Xepto50 scoring system provides a nuanced metric for drug efficacy. The findings underscore the modulation of molecular interactions and cellular responses by Y842 mutations in FLT3-KD, highlighting the need for tailored therapeutic approaches in FLT3-ITD-related malignancies.
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Affiliation(s)
- Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, 22381 Lund, Sweden
| | - Lina Al Ashiri
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, 22381 Lund, Sweden
| | - Rituraj Purohit
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India;
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, 22381 Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, 22185 Lund, Sweden
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18
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Nguyen D, Wu J, Corrigan P, Li Y. Computational investigation on lipid bilayer disruption induced by amphiphilic Janus nanoparticles: combined effect of Janus balance and charged lipid concentration. NANOSCALE 2023; 15:16112-16130. [PMID: 37753922 DOI: 10.1039/d3nr00403a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Janus nanoparticles (NPs) with charged/hydrophobic compartments have garnered attention for their potential antimicrobial activity. These NPs have been shown to disrupt lipid bilayers in experimental studies, yet the underlying mechanisms of this disruption at the particle-membrane interface remain unclear. To address this knowledge gap, the present study conducts a computational investigation to systematically examine the disruption of lipid bilayers induced by amphiphilic Janus NPs. The focus of this study is on the combined effects of the hydrophobicity of the Janus NP, referred to as the Janus balance, defined as the ratio of hydrophilic to hydrophobic surface coverage, and the concentration of charged phospholipids on the interactions between Janus NPs and lipid bilayers. Computational simulations were conducted using a coarse-grained molecular dynamics (MD) approach. The results of these MD simulations reveal that while the area change of the bilayer increases monotonically with the Janus balance, the effect of charged lipid concentration in the membrane is not easy to be predicted. Specifically, it was found that the concentration of negatively charged lipids is directly proportional to the intensity of membrane disruption. Conversely, positively charged lipids have a negligible effect on membrane defects. This study provides molecular insights into the significant role of Janus balance in the disruption of lipid bilayers by Janus NPs and supports the selectivity of Janus NPs for negatively charged lipid membranes. Furthermore, the anisotropic properties of Janus NPs were found to play a crucial role in their ability to disrupt the membrane via the combination of hydrophobic and electrostatic interactions. This finding is validated by testing the current Janus NP design on a bacterial membrane-mimicking model. This computational study may serve as a foundation for further studies aimed at optimizing the properties of Janus NPs for specific antimicrobial applications.
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Affiliation(s)
- Danh Nguyen
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - James Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Patrick Corrigan
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Ying Li
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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19
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Shi X, Li L, Liu Z, Wang F, Huang H. Exploring the mechanism of metformin action in Alzheimer's disease and type 2 diabetes based on network pharmacology, molecular docking, and molecular dynamic simulation. Ther Adv Endocrinol Metab 2023; 14:20420188231187493. [PMID: 37780174 PMCID: PMC10540612 DOI: 10.1177/20420188231187493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/19/2023] [Indexed: 10/03/2023] Open
Abstract
Background Metformin, which has been shown to be highly effective in treating type 2 diabetes (T2D), is also believed to be valuable for Alzheimer's disease (AD). Computer simulation techniques have emerged as an innovative approach to explore mechanisms. Objective To study the potential mechanism of metformin action in AD and T2D. Methods The chemical structure of metformin was obtained from PubChem. The targets of metformin were obtained from PubChem, Pharm Mapper, Batman, SwissTargetPrediction, DrugBank, and PubMed. The pathogenic genes of AD and T2D were retrieved from the GeneCards, OMIM, TTD, Drugbank, PharmGKB, and DisGeNET. The intersection of metformin with the targets of AD and T2D is represented by a Venn diagram. The protein-protein interaction (PPI) and core targets networks of intersected targets were constructed by Cytoscape 3.7.1. The enrichment information of GO and Kyoto Encyclopedia of Gene and Genomics (KEGG) pathways obtained by the Metascape was made into a bar chart and a bubble diagram. AutoDockTools, Pymol, and Chem3D were used for the molecular docking. Gromacs software was used to perform molecular dynamics (MD) simulation of the best binding target protein. Results A total of 115 key targets of metformin for AD and T2D were obtained. GO analysis showed that biological process mainly involved response to hormones and the regulation of ion transport. Cellular component was enriched in the cell body and axon. Molecular function mainly involved kinase binding and signal receptor regulator activity. The KEGG pathway was mainly enriched in pathways of cancer, neurodegeneration, and endocrine resistance. Core targets mainly included TP53, TNF, VEGFA, HIF1A, IL1B, IGF1, ESR1, SIRT1, CAT, and CXCL8. The molecular docking results showed best binding of metformin to CAT. MD simulation further indicated that the CAT-metformin complex could bind well and converge relatively stable at 30 ns. Conclusion Metformin exerts its effects on regulating oxidative stress, gluconeogenesis and inflammation, which may be the mechanism of action of metformin to improve the common pathological features of T2D and AD.
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Affiliation(s)
- Xin Shi
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Lingling Li
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Zhiyao Liu
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Fangqi Wang
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Hailiang Huang
- Shandong University of Traditional Chinese Medicine, 4655 Guyunhu Street, Changqing District, Jinan City, Shandong Province, China
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20
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Challapa-Mamani MR, Tomás-Alvarado E, Espinoza-Baigorria A, León-Figueroa DA, Sah R, Rodriguez-Morales AJ, Barboza JJ. Molecular Docking and Molecular Dynamics Simulations in Related to Leishmania donovani: An Update and Literature Review. Trop Med Infect Dis 2023; 8:457. [PMID: 37888585 PMCID: PMC10610989 DOI: 10.3390/tropicalmed8100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
Leishmaniasis, a disease caused by Leishmania parasites and transmitted via sandflies, presents in two main forms: cutaneous and visceral, the latter being more severe. With 0.7 to 1 million new cases each year, primarily in Brazil, diagnosing remains challenging due to diverse disease manifestations. Traditionally, the identification of Leishmania species is inferred from clinical and epidemiological data. Advances in disease management depend on technological progress and the improvement of parasite identification programs. Current treatments, despite the high incidence, show limited efficacy due to factors like cost, toxicity, and lengthy regimens causing poor adherence and resistance development. Diagnostic techniques have improved but a significant gap remains between scientific progress and application in endemic areas. Complete genomic sequence knowledge of Leishmania allows for the identification of therapeutic targets. With the aid of computational tools, testing, searching, and detecting affinity in molecular docking are optimized, and strategies that assess advantages among different options are developed. The review focuses on the use of molecular docking and molecular dynamics (MD) simulation for drug development. It also discusses the limitations and advancements of current treatments, emphasizing the importance of new techniques in improving disease management.
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Affiliation(s)
- Mabel R. Challapa-Mamani
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo 13007, Peru;
- Sociedad Científica de Estudiantes de Medicina de la Universidad César Vallejo, Trujillo 13007, Peru
| | - Eduardo Tomás-Alvarado
- Hospital General Regional 17, Instituto Mexicano del Seguro Social, Cancún 75533, Mexico;
| | | | | | - Ranjit Sah
- Department of Clinical Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 44600, Nepal;
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune 411018, Maharashtra, India
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima 150152, Peru;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 350000, Lebanon
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21
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Atiya A, Batra S, Mohammad T, Alorfi NM, Abdulmonem WA, Alhumaydhi FA, Ashraf GM, Baeesa SS, Elasbali AM, Shahwan M. Desmodin and isopongachromene as potential inhibitors of cyclin-dependent kinase 5: phytoconstituents targeting anticancer and neurological therapy. J Biomol Struct Dyn 2023; 41:8042-8052. [PMID: 36184739 DOI: 10.1080/07391102.2022.2128877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/20/2022] [Indexed: 10/07/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine-threonine protein kinase vital for neuronal cell cycle arrest and differentiation. It activates by binding with p35 and p39 and is important for the functioning of the nervous system. A growing body of evidence suggests that CDK5 contributes to the onset and progression of neurodegeneration and tumorigenesis and represents itself as a potential therapeutic target. Our research illustrates virtual screening of phytochemicals from the IMPPAT (Indian Medicinal Plants, Phytochemistry and Therapeutics) library to search for potential inhibitors of CDK5. Initially, the compounds from the parent library were filtered out via their physicochemical properties following the Lipinski rule of five. Then sequentially, molecular docking-based virtual screening, PAINS filter, ADMET, PASS analysis, and molecular dynamics (MD) simulation were done using various computational tools to rule out adversities that can cause hindrances in the identification of potential inhibitors of CDK5. Finally, two compounds were selected via the extensive screening showing significant binding with CDK5 ATP-binding pocket and ultimately were selected as potent ATP-competitive inhibitors of CDK5. Finally, we propose that the elucidated compounds Desmodin and Isopongachromene can be used further in the drug discovery process and act as therapeutics in the medical industry to treat certain complex diseases, including cancer and neurodegeneration.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Shivani Batra
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nasser M Alorfi
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Kingdom of Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saleh S Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Moyad Shahwan
- College of Pharmacy, Ajman University, Abha, United Arab Emirates
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Abha, United Arab Emirates
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22
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Ghadirian F, Abbasi H, Bavi O, Naeimabadi A. How living cells are affected during the cold atmospheric pressure plasma treatment. Free Radic Biol Med 2023; 205:141-150. [PMID: 37295538 DOI: 10.1016/j.freeradbiomed.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
When the electric discharge process is limited by high voltage electrodes shielding, the ionization measure would be controlled to less than one percent and the temperature to less than 37 °C even at atmospheric pressure, so-called cold atmospheric pressure plasma (CAP). CAP has been found to have profound medical applications in association with its reactive oxygen and nitrogen species (ROS/RNS). In this way that during plasma exposure, the subjected medium (e.g. cell cytoplasmic membrane in plasma therapy) interacts with ROS/RNS. Accordingly, a precise study of the mentioned interactions and their consequences on the cells' behavior changes, is necessary. The results lead to the reduction of possible risks and provide the opportunity of optimizing the efficacy of CAP before the development of CAP applications in the field of plasma medicine. In this report molecular dynamic (MD) simulation is used to investigate the mentioned interactions and a proper and compatible comparison with the experimental results is presented. Based on this, the effects of H2O2, NO and O2 on the living cell's membrane are investigated in biological conditions. Our results show that: i) The hydration of phospholipid polar heads would be enhanced associated with the H2O2 presence. ii) A new definition of the surface area assigned to each phospholipid (APL), more reliable and compatible with the physical expectations, is introduced. iii) The long-term behavior of NO and O2 is their penetration into the lipid bilayer and sometimes passing through the membrane into the cell. The latter would be an indication of internal cells' pathways activation leading to modification of cells' function.
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Affiliation(s)
- Fatemeh Ghadirian
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
| | - Hossein Abbasi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Aboutorab Naeimabadi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
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23
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Kuang Y, Ma X, Shen W, Rao Q, Yang S. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci OA 2023; 9:FSO853. [PMID: 37090493 PMCID: PMC10116374 DOI: 10.2144/fsoa-2023-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Coronavirus main protease (3CLpro), a special cysteine protease in coronavirus family, is highly desirable in the life cycle of coronavirus. Here, molecular docking, ADMET pharmacokinetic profiles and molecular dynamics (MD) simulation were performed to develop specific 3CLpro inhibitor. The results showed that the 137 compounds originated from Chinese herbal have good binding affinity to 3CLpro. Among these, Cleomiscosin C, (+)-Norchelidonine, Protopine, Turkiyenine, Isochelidonine and Mallotucin A possessed prominent drug-likeness properties. Cleomiscosin C and Turkiyenine exhibited excellent pharmacokinetic profiles. Furthermore, the complex of Cleomiscosin C with SARS-CoV-2 main protease presented high stability. The findings in this work indicated that Cleomiscosin C is highly promising as a potential 3CLpro inhibitor, thus facilitating the development of effective drugs for COVID-19.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
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24
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Johnson TO, Akinsanmi AO, Ejembi SA, Adeyemi OE, Oche JR, Johnson GI, Adegboyega AE. Modern drug discovery for inflammatory bowel disease: The role of computational methods. World J Gastroenterol 2023; 29:310-331. [PMID: 36687123 PMCID: PMC9846937 DOI: 10.3748/wjg.v29.i2.310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) comprising ulcerative colitis, Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract. IBD has spread around the world and is becoming more prevalent at an alarming rate in developing countries whose societies have become more westernized. Cell therapy, intestinal microecology, apheresis therapy, exosome therapy and small molecules are emerging therapeutic options for IBD. Currently, it is thought that low-molecular-mass substances with good oral bio-availability and the ability to permeate the cell membrane to regulate the action of elements of the inflammatory signaling pathway are effective therapeutic options for the treatment of IBD. Several small molecule inhibitors are being developed as a promising alternative for IBD therapy. The use of highly efficient and time-saving techniques, such as computational methods, is still a viable option for the development of these small molecule drugs. The computer-aided (in silico) discovery approach is one drug development technique that has mostly proven efficacy. Computational approaches when combined with traditional drug development methodology dramatically boost the likelihood of drug discovery in a sustainable and cost-effective manner. This review focuses on the modern drug discovery approaches for the design of novel IBD drugs with an emphasis on the role of computational methods. Some computational approaches to IBD genomic studies, target identification, and virtual screening for the discovery of new drugs and in the repurposing of existing drugs are discussed.
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Affiliation(s)
| | | | | | | | - Jane-Rose Oche
- Department of Biochemistry, University of Jos, Jos 930222, Plateau, Nigeria
| | - Grace Inioluwa Johnson
- Faculty of Clinical Sciences, College of Health Sciences, University of Jos, Jos 930222, Plateau, Nigeria
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25
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Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
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26
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Morales BGDV, Dos Reis MC, Gomes TJDS, Zeferino NA, de Oliveira GA, Zanchi FB. A rational in silico approach to identify inhibitors of Batroxrhagin from Bothrops atrox. J Biomol Struct Dyn 2022; 40:9620-9635. [PMID: 34060428 DOI: 10.1080/07391102.2021.1932597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bothrops atrox venom comprises several types of bioactive molecules, enzymatic and non-enzymatic, among those, Batroxrhagin is the most predominant SVMP P-III enzyme, which are responsible for induction of local and systemic hemorrhage and muscle fibers damage, impairing regeneration. Due to great difficulties in establishing an antibothropic drug, new strategies must be addressed to achieve a more effective and efficient treatment. There are no studies of specific catalytic inhibitors of Batroxrhagin. However, there are in vitro studies that have described similar metalloprotease inhibitors. The inhibitor batimastat was used as a leading compound for the search and selection of similar candidates. This molecule is widely cited as a metalloprotease inhibitor and as an antimetastatic. In addition to batimastat-like molecules, four other reported metalloprotease inhibitors were included to compose the study's positive control group. Hence, 580 molecules were tested. The three-dimensional structure of B. atrox Batroxrhagin was predicted based on homologous structures using Modeller 9.20. Molecular docking calculation was performed using Autodock 4.2 and molecular surfaces and interactions were analyzed using Biovia/Discovery Studio 2017. Among 576 molecules, 42 similar to batismast resulted in a better energy of interaction than all positive controls, including batimastat itself. The batimastat-like molecules with lowest energy and positive controls were subjected to molecular dynamics for 30 ns in Gromacs 2019.4. This batimastat-like molecule produced better stability among all the Batroxrhagin-ligand complexes analyzed. Overall, the proposed compounds present justifiable evidence for future in vitro tests aiming to inhibit Batroxrhagin. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno Gildo Dalla Vecchia Morales
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho-RO, Brazil.,FIOCRUZ Rondônia, Porto Velho-RO, Brazil
| | - Marlon Chaves Dos Reis
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Faculdades Integradas Aparício Carvalho/FIMCA, Porto Velho-RO, Brazil
| | | | - Nabia Azevedo Zeferino
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Faculdades Integradas Aparício Carvalho/FIMCA, Porto Velho-RO, Brazil
| | - George Azevedo de Oliveira
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Doutorado em Ciências - Cooperação IOC/Fiocruz Rondônia: Biologia Computacional e Sistemas (BCS), Porto Velho-RO, Brazil
| | - Fernando Berton Zanchi
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho-RO, Brazil.,FIOCRUZ Rondônia, Porto Velho-RO, Brazil.,Programa de Doutorado em Ciências - Cooperação IOC/Fiocruz Rondônia: Biologia Computacional e Sistemas (BCS), Porto Velho-RO, Brazil.,Instituto Nacional de Epidemiologia na Amazônia Ocidental - EPIAMO, Porto Velho-RO, Brazil
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27
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Singh K, Muttathukattil AN, Singh PC, Reddy G. pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations. J Phys Chem B 2022; 126:9759-9770. [PMID: 36383764 DOI: 10.1021/acs.jpcb.2c05117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm+) to the active site of hen egg-white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm+ moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm+ binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm+ binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest pKa of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm+ can bind at the active site, with the Gdm+ bound in the cavity of the active site acting as a scaffold for the other two Gdm+ ions binding. These results can aid in providing greater insights into designing novel molecules containing Gdm+ moieties that can have high binding affinities to inhibit the function of enzymes with acidic residues in their active site.
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Affiliation(s)
- Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru560012, Karnataka, India
| | - Aswathy N Muttathukattil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru560012, Karnataka, India
| | - Prashant Chandra Singh
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru560012, Karnataka, India
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28
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Searching glycolate oxidase inhibitors based on QSAR, molecular docking, and molecular dynamic simulation approaches. Sci Rep 2022; 12:19969. [PMID: 36402831 PMCID: PMC9675741 DOI: 10.1038/s41598-022-24196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Primary hyperoxaluria type 1 (PHT1) treatment is mainly focused on inhibiting the enzyme glycolate oxidase, which plays a pivotal role in the production of glyoxylate, which undergoes oxidation to produce oxalate. When the renal secretion capacity exceeds, calcium oxalate forms stones that accumulate in the kidneys. In this respect, detailed QSAR analysis, molecular docking, and dynamics simulations of a series of inhibitors containing glycolic, glyoxylic, and salicylic acid groups have been performed employing different regression machine learning techniques. Three robust models with less than 9 descriptors-based on a tenfold cross (Q2 CV) and external (Q2 EXT) validation-were found i.e., MLR1 (Q2 CV = 0.893, Q2 EXT = 0.897), RF1 (Q2 CV = 0.889, Q2 EXT = 0.907), and IBK1 (Q2 CV = 0.891, Q2 EXT = 0.907). An ensemble model was built by averaging the predicted pIC50 of the three models, obtaining a Q2 EXT = 0.933. Physicochemical properties such as charge, electronegativity, hardness, softness, van der Waals volume, and polarizability were considered as attributes to build the models. To get more insight into the potential biological activity of the compouds studied herein, docking and dynamic analysis were carried out, finding the hydrophobic and polar residues show important interactions with the ligands. A screening of the DrugBank database V.5.1.7 was performed, leading to the proposal of seven commercial drugs within the applicability domain of the models, that can be suggested as possible PHT1 treatment.
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29
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Rieder SR, Ries BJ, Kubincová A, Champion C, Barros EP, Hünenberger PH, Riniker S. Leveraging the Sampling Efficiency of RE-EDS in OpenMM Using a Shifted Reaction-Field With an Atom-Based Cutoff. J Chem Phys 2022; 157:104117. [DOI: 10.1063/5.0107935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Replica-exchange enveloping distribution sampling (RE-EDS) is a pathway-independent multistate free-energy method, currently implemented in the GROMOS software package for molecular dynamics (MD) simulations. It has a high intrinsic sampling efficiency as the interactions between the unperturbed particles have to be calculated only once for multiple end-states. As a result, RE-EDS is an attractive method for the calculation of relative solvation and binding free energies. An essential requirement for reaching this high efficiency is the separability of the nonbonded interactions into solute-solute, solute-environment, and environment-environment contributions. Such a partitioning is trivial when using a Coulomb term with a reaction-field (RF) correction to model the electrostatic interactions, but not when using lattice- sum schemes. To avoid cutoff artifacts, the RF correction is typically used in combination with a charge-group based cutoff, which is not supported by most small-molecule force fields and other MD engines. To address this issue, we investigate the combination of RE-EDS simulations with a recently introduced RF scheme including a shifting function that enables the rigorous calculation of RF electrostatics with atom-based cutoffs. The resulting approach is validated by calculating solvation free energies with the generalized AMBER force field (GAFF) in water and chloroform using both the GROMOS software package and a proof-of-concept implementation in OpenMM.
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Affiliation(s)
| | | | | | | | | | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich D-CHAB, Switzerland
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30
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Ogunyemi OM, Gyebi GA, Saheed A, Paul J, Nwaneri-Chidozie V, Olorundare O, Adebayo J, Koketsu M, Aljarba N, Alkahtani S, Batiha GES, Olaiya CO. Inhibition mechanism of alpha-amylase, a diabetes target, by a steroidal pregnane and pregnane glycosides derived from Gongronema latifolium Benth. Front Mol Biosci 2022; 9:866719. [PMID: 36032689 PMCID: PMC9399641 DOI: 10.3389/fmolb.2022.866719] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/07/2022] [Indexed: 12/23/2022] Open
Abstract
Alpha-amylase is widely exploited as a drug target for preventing postprandial hyperglycemia in diabetes and other metabolic diseases. Inhibition of this enzyme by plant-derived pregnanes is not fully understood. Herein, we used in vitro, in silico, and in vivo studies to provide further insights into the alpha-amylase inhibitory potential of selected pregnane-rich chromatographic fractions and four steroidal pregnane phytochemicals (SPPs), viz: marsectohexol (P1), 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→14)-β-D-oleandropyranosyl]-11,12-di-O-tigloyl-17β-marsdenin (P2), 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β-marsdenin (P3), and 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-canaropyranosyl]-17β-marsdenin (P4) derived from Gongronema latifolium Benth. The results revealed that the SPPs source pregnane-rich chromatographic fractions and the SPPs (P1–P4) exhibited inhibitory potential against porcine pancreatic alpha-amylase in vitro. Compounds P1 and P2 with IC50 values 10.01 and 12.10 µM, respectively, showed greater inhibitory potential than the reference acarbose (IC50 = 13.47 µM). Molecular docking analysis suggests that the SPPs had a strong binding affinity to porcine pancreatic alpha-amylase (PPA), human pancreatic alpha-amylase (HPA), and human salivary alpha-amylase (HSA), interacting with the key active site residues through an array of hydrophobic interactions and hydrogen bonds. The strong interactions of the SPPs with Glu233 and Asp300 residues may disrupt their roles in the acid-base catalytic mechanism and proper orientation of the polymeric substrates, respectively. The interactions with human pancreatic amylase were maintained in a dynamic environment as indicated by the root mean square deviation, radius of gyration, surface accessible surface area, and number of hydrogen bonds computed from the trajectories obtained from a 100-ns molecular dynamics simulation. Key loop regions of HPA that contribute to substrate binding exhibited flexibility and interaction potential toward the compounds as indicated by the root mean square fluctuation. Furthermore, P1 significantly reduced blood glucose levels and area under the curve in albino rats which were orally challenged with starch. Therefore, Gongronema latifolium and its constituent SPPs may be exploited as inhibitors of pancreatic alpha-amylase as an oral policy for impeding postprandial blood glucose rise.
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Affiliation(s)
- Oludare M. Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
- Nutritional and Industrial Biochemistry Unit, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
- *Correspondence: Oludare M. Ogunyemi, ; Gideon A. Gyebi,
| | - Gideon A. Gyebi
- Department of Biochemistry, Faculty of Science and Technology Bingham University, Nasarawa, Nigeria
- Natural Products and Structural (Bio-Chem)-informatics Research Laboratory (NpsBC-Rl), Bingham University, Nasarawa, Nigeria
- *Correspondence: Oludare M. Ogunyemi, ; Gideon A. Gyebi,
| | - Afolabi Saheed
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Jesse Paul
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Victoria Nwaneri-Chidozie
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Olufunke Olorundare
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Joseph Adebayo
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Mamoru Koketsu
- Faculty of Engineering, Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Nada Aljarba
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Charles O. Olaiya
- Nutritional and Industrial Biochemistry Unit, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
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31
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Rieder SR, Ries B, Schaller K, Champion C, Barros EP, Hünenberger PH, Riniker S. Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. J Chem Inf Model 2022; 62:3043-3056. [PMID: 35675713 PMCID: PMC9241072 DOI: 10.1021/acs.jcim.2c00383] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Free-energy differences
between pairs of end-states can be estimated
based on molecular dynamics (MD) simulations using standard pathway-dependent
methods such as thermodynamic integration (TI), free-energy perturbation,
or Bennett’s acceptance ratio. Replica-exchange enveloping
distribution sampling (RE-EDS), on the other hand, allows for the
sampling of multiple end-states in a single simulation without the
specification of any pathways. In this work, we use the RE-EDS method
as implemented in GROMOS together with generalized AMBER force-field
(GAFF) topologies, converted to a GROMOS-compatible format with a
newly developed GROMOS++ program amber2gromos, to
compute relative hydration free energies for a series of benzene derivatives.
The results obtained with RE-EDS are compared to the experimental
data as well as calculated values from the literature. In addition,
the estimated free-energy differences in water and in vacuum are compared
to values from TI calculations carried out with GROMACS. The hydration
free energies obtained using RE-EDS for multiple molecules are found
to be in good agreement with both the experimental data and the results
calculated using other free-energy methods. While all considered free-energy
methods delivered accurate results, the RE-EDS calculations required
the least amount of total simulation time. This work serves as a validation
for the use of GAFF topologies with the GROMOS simulation package
and the RE-EDS approach. Furthermore, the performance of RE-EDS for
a large set of 28 end-states is assessed with promising results.
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Affiliation(s)
- Salomé R Rieder
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin Ries
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Kay Schaller
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Candide Champion
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Emilia P Barros
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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32
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In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19. Int J Mol Sci 2022; 23:ijms23136889. [PMID: 35805893 PMCID: PMC9267096 DOI: 10.3390/ijms23136889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Treatment options for Coronavirus Disease 2019 (COVID-19) remain limited, and the option of repurposing approved drugs with promising medicinal properties is of increasing interest in therapeutic approaches to COVID-19. Using computational approaches, we examined griseofulvin and its derivatives against four key anti-SARS-CoV-2 targets: main protease, RdRp, spike protein receptor-binding domain (RBD), and human host angiotensin-converting enzyme 2 (ACE2). Molecular docking analysis revealed that griseofulvin (CID 441140) has the highest docking score (–6.8 kcal/mol) with main protease of SARS-CoV-2. Moreover, griseofulvin derivative M9 (CID 144564153) proved the most potent inhibitor with −9.49 kcal/mol, followed by A3 (CID 46844082) with −8.44 kcal/mol against M protease and ACE2, respectively. Additionally, H bond analysis revealed that compound A3 formed the highest number of hydrogen bonds, indicating the strongest inhibitory efficacy against ACE2. Further, molecular dynamics (MD) simulation analysis revealed that griseofulvin and these derivatives are structurally stable. These findings suggest that griseofulvin and its derivatives may be considered when designing future therapeutic options for SARS-CoV-2 infection.
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33
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Bai Q, Liu S, Tian Y, Xu T, Banegas‐Luna AJ, Pérez‐Sánchez H, Huang J, Liu H, Yao X. Application advances of deep learning methods for de novo drug design and molecular dynamics simulation. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1581] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Qifeng Bai
- Key Lab of Preclinical Study for New Drugs of Gansu Province Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University Lanzhou Gansu China
| | - Shuo Liu
- School of Pharmacy Lanzhou University Lanzhou Gansu China
| | - Yanan Tian
- School of Pharmacy Lanzhou University Lanzhou Gansu China
| | - Tingyang Xu
- Tencent AI Lab, Shenzhen Tencent Computer Ltd Shenzhen China
| | - Antonio Jesús Banegas‐Luna
- Structural Bioinformatics and High Performance Computing Research Group (BIO‐HPC), Computer Engineering Department UCAM Universidad Católica de Murcia Murcia Spain
| | - Horacio Pérez‐Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO‐HPC), Computer Engineering Department UCAM Universidad Católica de Murcia Murcia Spain
| | - Junzhou Huang
- Tencent AI Lab, Shenzhen Tencent Computer Ltd Shenzhen China
| | - Huanxiang Liu
- School of Pharmacy Lanzhou University Lanzhou Gansu China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering Lanzhou University Lanzhou Gansu China
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34
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Khanal SP, Adhikari NP. Thermodynamic and transport properties of amoxicillin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Trapl D, Krupička M, Višňovský V, Hozzová J, Ol'ha J, Křenek A, Spiwok V. Property Map Collective Variable as a Useful Tool for a Force Field Correction. J Chem Inf Model 2022; 62:567-576. [PMID: 35112877 DOI: 10.1021/acs.jcim.1c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accuracy of biomolecular simulations depends on the accuracy of an empirical molecular mechanics potential known as a force field: a set of parameters and expressions to estimate the potential from atomic coordinates. Accurate parametrization of force fields for small organic molecules is a challenge due to their high diversity. One of the possible approaches is to apply a correction to the existing force fields. Here, we propose an approach to estimate the density functional theory (DFT)-derived force field correction which is calculated during the run of molecular dynamics without significantly affecting its speed. Using the formula known as a property map collective variable, we approximate the force field correction by a weighted average of this force field correction calculated only for a small series of reference structures. To validate this method, we used seven AMBER force fields, and we show how it is possible to convert one force field to behave like the other one. We also present the force field correction for the important anticancer drug Imatinib as a use case example. Our method appears to be suitable for adjusting the force field for general drug-like molecules. We provide a pipeline that generates the correction; this pipeline is available at https://pmcvff-correction.cerit-sc.cz/.
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Affiliation(s)
- Dalibor Trapl
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - Martin Krupička
- Department of Organic Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - Vladimír Višňovský
- Institute of Computer Science, Masaryk University, Botanická 554/68a, Brno 602 00, Czech Republic
| | - Jana Hozzová
- Institute of Computer Science, Masaryk University, Botanická 554/68a, Brno 602 00, Czech Republic
| | - Jaroslav Ol'ha
- Institute of Computer Science, Masaryk University, Botanická 554/68a, Brno 602 00, Czech Republic
| | - Aleš Křenek
- Institute of Computer Science, Masaryk University, Botanická 554/68a, Brno 602 00, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
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36
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Fadaka AO, Sibuyi NRS, Madiehe AM, Meyer M. Computational insight of dexamethasone against potential targets of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:875-885. [PMID: 32924825 PMCID: PMC7544935 DOI: 10.1080/07391102.2020.1819880] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
The health sector has been on the race to find a potent therapy for coronavirus disease (COVID)-19, a diseases caused by severe acute respiratory syndrome coronavirus (SARS-CoV)-2. Repurposed anti-viral drugs have played a huge role in combating the virus, and most recently, dexamethasone (Dex) have shown its therapeutic activity in severe cases of COVID-19 patients. The study sought to provide insights on the anti-COVID-19 mechanism of Dex at both atomic and molecular level against SARS-CoV-2 targets. Computational methods were employed to predict the binding affinity of Dex to SARS-CoV-2 using the Schrodinger suite (v2020-2). The target molecules and ligand (Dex) were retrieved from PDB and PubChem, respectively. The selected targets were SARS-CoV-2 main protease (Mpro), and host secreted molecules glucocorticoid receptor, and Interleukin-6 (IL-6). Critical analyses such as Protein and ligand preparation, molecular docking, molecular dynamic (MD) simulations, and absorption, distribution, metabolism, excretion (ADME), and toxicity analyses were performed using the targets and the ligand as inputs. Dex showed stronger affinity to its theoretical (glucocorticoid) receptor with a superior docking score of -14.7 and a good binding energy value of -147.48 kcal/mol; while short hydrogen bond distances were observed in both Mpro and IL-6 when compared to glucocorticoid receptor. Based on these findings, Dex-target complexes were used to perform MD simulations to analyze Dex stability at 50 ns. This study demonstrates that Dex could bind to both the viral and host receptors as a potential drug candidate for COVID-19. To ascertain the biological fitness of this study, other SARS-CoV-2 targets should be explored. Also, the in vitro studies of dexamethasone against several SARS-CoV-2 targets warrant further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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37
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Calculation of Crystal-Solution Dissociation Constants. Biomolecules 2022; 12:biom12020147. [PMID: 35204648 PMCID: PMC8961641 DOI: 10.3390/biom12020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics simulations, but this approach is very computationally expensive, and entropy calculations are especially slow. We develop an alternative very fast method of calculating the binding entropy and dissociation constants. The main part of our approach is based on the evaluation of movement ranges of molecules in the bound state. Then, the range of molecular movements in the bound state (here, in molecular crystals) is used for the calculation of the binding entropies and, then (using, in addition, the experimentally measured sublimation enthalpies), the crystal-to-vapor dissociation constants. Previously, we considered the process of the reversible sublimation of small organic molecules from crystals to vapor. In this work, we extend our approach by considering the dissolution of molecules, in addition to their sublimation. Similar to the sublimation case, our method shows a good correlation with experimentally measured dissociation constants at the dissolution of crystals.
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38
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Jawad B, Adhikari P, Cheng K, Podgornik R, Ching WY. Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. Int J Mol Sci 2022; 23:838. [PMID: 35055023 PMCID: PMC8776159 DOI: 10.3390/ijms23020838] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA;
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China;
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
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39
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Aghajani J, Farnia P, Farnia P, Ghanavi J, Velayati AA. Molecular Dynamic Simulations and Molecular Docking as a Potential Way for Designed New Inhibitor Drug without Resistance. TANAFFOS 2022; 21:1-14. [PMID: 36258912 PMCID: PMC9571241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/30/2021] [Indexed: 06/16/2023]
Abstract
Mycobacterium tuberculosis is the cause of tuberculosis in humans and is responsible for more than 2 million deaths per year. Despite the development of anti-tuberculosis drugs (Isoniazid, Rifampicin, Ethambutol, pyrazinamide, streptomycin, etc.) and the TB vaccine, this disease has claimed the lives of many people around the world. Drug resistance in this disease is increasing day by day. Conventional methods for discovering and developing drugs are usually time-consuming and expensive. Therefore, a better method is needed to identify, design, and manufacture TB drugs without drug resistance. Bioinformatics applications in obtaining new drugs at the structural level include studies of the mechanism of drug resistance, detection of drug interactions, and prediction of mutant protein structure. In the present study, computer-based approaches including molecular dynamics simulation and molecular docking as a novel and efficient method for the identification and investigation of new cases as well as the investigation of mutated proteins and compounds will be examined .
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Affiliation(s)
- Jafar Aghajani
- Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Poopak Farnia
- Department of Biotechnology, School of Advanced Technology in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalaledin Ghanavi
- Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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40
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Dobhal A, Srivastav A, Dandekar P, Jain R. Influence of lactide vs glycolide composition of poly (lactic-co-glycolic acid) polymers on encapsulation of hydrophobic molecules: molecular dynamics and formulation studies. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2021; 32:126. [PMID: 34591178 PMCID: PMC8484083 DOI: 10.1007/s10856-021-06580-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The work demonstrates the preparation of PLGA (PLGA 50:50, PLGA 75:25) nanoparticles, to encapsulate a hydrophobic molecule (coumarin-6), using the microreactor-based continuous process. The formulations were characterized using dynamic light scattering and transmission electron microscopy to determine their size, homogeneity, zeta potential, and surface morphology. The resulting nanoparticles were safe to the CHO cells (≈80% cell survival), at the concentration of ≤600 µg/mL and were successfully taken up by the cells, as demonstrated using confocal microscopy. Moreover, imaging flow cytometry confirmed that the nanoparticles were internalized in 73.96% of the cells. Furthermore, molecular dynamics simulation and docking studies were carried out to explore the effect of polymer chain length of PLGA and lactide vs glycolide (LA:GA) ratio on their compatibility with the coumarin-6 molecules and to study the coiling and flexibility of PLGA in the presence of coumarin-6 molecules. Flory-Huggins interaction parameter (χ) was calculated for polymer chains of varying lengths and LA:GA ratio, with respect to coumarin-6. χ parameter increased with increase in polymer chain length, which indicated superior interaction of coumarin-6 with the smaller chains. Amongst all the polymeric systems, PLGA55 exhibited the strongest interaction with coumarin-6, for all the chain lengths, possibly because of their homogeneous spatial arrangements and superior binding energy. PLGA27 showed better compatibility compared to PLGA72 and PGA, whereas PLA-based polymers exhibited the least compatibility. Analysis of the radius of gyration of the polymer chains in the polymer-coumarin-6 complexes, at the end of molecular dynamics run, exhibited that the polymer chains displayed varying coiling behavior and flexibility, depending upon the relative concentrations of the polymer and coumarin-6. Factors like intra-chain interactions, spatial arrangement, inter-chain binding energies, and polymer-coumarin-6 compatibility also influenced the coiling and flexibility of polymer chains.
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Affiliation(s)
- Anurag Dobhal
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Ashu Srivastav
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
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41
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Zavitsanou S, Tsengenes A, Papadourakis M, Amendola G, Chatzigoulas A, Dellis D, Cosconati S, Cournia Z. FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations. J Chem Inf Model 2021; 61:4131-4138. [PMID: 34519200 DOI: 10.1021/acs.jcim.1c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/.
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Affiliation(s)
- Stamatia Zavitsanou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece.,Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Alexandros Tsengenes
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Michail Papadourakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Giorgio Amendola
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece.,Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Dimitris Dellis
- Greek Research and Technology Network, S.A., 7 Kifissias Avenue, 11523 Athens, Greece
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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42
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Liu Q, Wang D, Yu M, Cong B, Yu X. The influences of electric field intensity and driving force on the slip behaviour of water flow in a nanochannel. PLoS One 2021; 16:e0257589. [PMID: 34551001 PMCID: PMC8457446 DOI: 10.1371/journal.pone.0257589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/05/2021] [Indexed: 11/18/2022] Open
Abstract
In the present work, non-equilibrium molecular dynamics (MD) simulations are used to investigate the flow of liquid water between two metallic solid atomistic smooth walls. The present work focuses on the combined effect of external electric field and driving force on the slip behaviour and structure of liquid water at the solid-water interface. The upper wall of the set model is positively charged, and the lower wall of the model is negatively charged. The simulation results show that as the driving force increases, the slip length also increases. At a given driving force, no matter how the electric field intensity changes, there is almost no change in the slip length, so the slip length is independent of the electric field strength. In addition, the results found that there is a linear relationship between the slip length and the normalised main peak of the static structure factor under different driving forces.
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Affiliation(s)
- Qiwei Liu
- Jilin Provincial Key Laboratory for Numerical Simulation, Jilin Normal University, Siping, Jilin, P. R. China
| | - Dezheng Wang
- Beijing Institute of Mechanical and Electrical Engineering, Beijing, P. R. China
| | - Miao Yu
- School of Materials Science and Engineering, Institute for Advanced Materials, Jiangsu University, Zhenjiang, P. R. China
| | - Biao Cong
- Jilin Provincial Key Laboratory for Numerical Simulation, Jilin Normal University, Siping, Jilin, P. R. China
- * E-mail: (BC); (XY)
| | - Xiaopeng Yu
- Jilin Provincial Key Laboratory for Numerical Simulation, Jilin Normal University, Siping, Jilin, P. R. China
- * E-mail: (BC); (XY)
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43
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Ahmad B, Batool M, Ain QU, Kim MS, Choi S. Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations. Int J Mol Sci 2021; 22:9124. [PMID: 34502033 PMCID: PMC8430524 DOI: 10.3390/ijms22179124] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 12/23/2022] Open
Abstract
The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoamide, lopinavir, and ritonavir to the coronavirus 3-chymotrypsin-like-protease (3CLpro) by means of docking and molecular dynamic (MD) simulations. The analysis of MD trajectories of 3CLpro with PF-07321332, α-ketoamide, lopinavir, and ritonavir revealed that 3CLpro-PF-07321332 and 3CLpro-α-ketoamide complexes remained stable compared with 3CLpro-ritonavir and 3CLpro-lopinavir. Investigating the dynamic behavior of ligand-protein interaction, ligands PF-07321332 and α-ketoamide showed stronger bonding via making interactions with catalytic dyad residues His41-Cys145 of 3CLpro. Lopinavir and ritonavir were unable to disrupt the catalytic dyad, as illustrated by increased bond length during the MD simulation. To decipher the ligand binding mode and affinity, ligand interactions with SARS-CoV-2 proteases and binding energy were calculated. The binding energy of the bespoke antiviral PF-07321332 clinical candidate was two times higher than that of α-ketoamide and three times than that of lopinavir and ritonavir. Our study elucidated in detail the binding mechanism of the potent PF-07321332 to 3CLpro along with the low potency of lopinavir and ritonavir due to weak binding affinity demonstrated by the binding energy data. This study will be helpful for the development and optimization of more specific compounds to combat coronavirus disease.
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Affiliation(s)
- Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (B.A.); (M.B.); (Q.u.A.); (M.S.K.)
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (B.A.); (M.B.); (Q.u.A.); (M.S.K.)
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon 16502, Korea
| | - Qurat ul Ain
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (B.A.); (M.B.); (Q.u.A.); (M.S.K.)
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (B.A.); (M.B.); (Q.u.A.); (M.S.K.)
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (B.A.); (M.B.); (Q.u.A.); (M.S.K.)
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon 16502, Korea
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44
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Exploring the cause of the dual allosteric targeted inhibition attaching to allosteric sites enhancing SHP2 inhibition. Mol Divers 2021; 26:1567-1580. [PMID: 34338914 DOI: 10.1007/s11030-021-10286-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
SHP2 is a protein tyrosine phosphatase (PTP) that can regulate the tyrosine phosphorylation level. Overexpression of SHP2 will promote the development of cancer diseases, so SHP2 has become one of the popular targets for the treatment of cancer. Studies have reported that both SHP099 and SHP844 are inhibitors of SHP2 and bind to different allosteric sites 1 and 2, respectively. Studies have shown that combining SHP099 with SHP844 will enhance pharmacological pathway inhibition in cells. This study uses molecular dynamic simulations to explore the dual allosteric targeted inhibition mechanism. The result shows that the residues THR108-TRP112 (allosteric site 1) move to LEU236-GLN245 (αB-αC link loop in PTP domain) , the residues of GLN79-GLN87 (allosteric site 2) get close to LEU262-GLN269 (αA-αB link loop in PTP domain) and HIS458-ARG465 (P-loop) come near to ARG501-THR507 (Q-loop) in SHP2-SHP099-SHP844 system, which makes the "inactive conformation" more stable and prevents the substrate from entering the catalytic site. Meanwhile, residue GLU110 (allosteric site 1), ARG265 (allosteric site 2), and ARG501 (Q-loop) are speculated to be the key residues that causing the SHP2 protein in auto-inhibition conformation. It is hoped that this study will provide clues for the development of the dual allosteric targeted inhibition of SHP2.
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45
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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46
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Vora J, Athar M, Sinha S, Jha PC, Shrivastava N. Binding Insight of Anti-HIV Phytocompounds with Prime Targets of HIV: A Molecular Dynamics Simulation Analysis. Curr HIV Res 2021; 18:132-141. [PMID: 31995010 DOI: 10.2174/1570162x18666200129112509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/27/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Despite intense efforts, AIDS is difficult to tackle by current anti-retroviral therapy (ART) due to its side effects; therefore, there is an urgent need to discover potential, multitarget and low-cost anti-HIV compounds. OBJECTIVE We have shown that few phytocompounds can potentially inhibit the prime targets of HIV namely GP120 envelope protein, reverse transcriptase, protease, integrase and ribonulcease. In this study, top ranked prioritized compounds were subjected to Molecular Dynamics (MD) simulation in order to study the conformational dynamics and integrity of crucial interaction in the receptor sites. METHODS The system was built for selected protein-ligand complex using TIP3P water model and OPLS_2005 force field. Trajectories were recorded up to 20 ns simulation time in Desmond module of Schrödinger software. RESULTS As a result of a comprehensive analysis of molecular properties and dynamics of the complexes, it has been concluded that Chebulic acid, Curcumin and Mulberroside C could be developed as envelope glycoprotein GP120 inhibitor, reverse transcriptase inhibitor and protease inhibitor respectively. However, the fluctuation of Chebulic acid with respect to integrase and ribonuclease protein was higher during the simulation. CONCLUSION These findings can aid in the designing of the structural properties for more effective anti-HIV compounds against the given targets.
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Affiliation(s)
- Jaykant Vora
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, Gujarat, India.,Department of Life Science, Gujarat University, Ahmedabad, Gujarat; India
| | - Mohd Athar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India
| | - Sonam Sinha
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, Gujarat, India.,Department of Life Science, Gujarat University, Ahmedabad, Gujarat; India
| | - Prakash C Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, Gujarat, India
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47
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Andoh Y, Ichikawa SI, Sakashita T, Yoshii N, Okazaki S. Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations. J Comput Chem 2021; 42:1073-1087. [PMID: 33780021 DOI: 10.1002/jcc.26524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
Abstract
In the era of exascale supercomputers, large-scale, and long-time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)-communication in the MPI-parallelized fast multipole method (FMM) combined with MD calculations under three-dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM. In communications of multipole coefficients, the reduction rate of communication data in the new algorithm relative to the amount of data in the conventional one increases as both the number of FMM levels and the number of MPI processes increase. The aforementioned rate increase could exceed 50% as the number of MPI processes becomes larger for very large systems. The proposed algorithm, named the minimum-transferred data (MTD) method, should enable large-scale and long-time MD calculations to be calculated efficiently, under the condition of massive MPI-parallelization on exascale supercomputers.
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Affiliation(s)
- Yoshimichi Andoh
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shin-Ichi Ichikawa
- Computational Science Division, Technical Computing Business Unit, Fujitsu Limited, Chiba, Japan
| | - Tatsuya Sakashita
- Department of Information and Communication Technology, College of Engineering, Tamagawa University, Machida, Tokyo, Japan
| | - Noriyuki Yoshii
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
- Department of Advanced Materials Science, The University of Tokyo, Kashiwa, Chiba, Japan
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48
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Thakore SD, Akhtar J, Jain R, Paudel A, Bansal AK. Analytical and Computational Methods for the Determination of Drug-Polymer Solubility and Miscibility. Mol Pharm 2021; 18:2835-2866. [PMID: 34041914 DOI: 10.1021/acs.molpharmaceut.1c00141] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the pharmaceutical industry, poorly water-soluble drugs require enabling technologies to increase apparent solubility in the biological environment. Amorphous solid dispersion (ASD) has emerged as an attractive strategy that has been used to market more than 20 oral pharmaceutical products. The amorphous form is inherently unstable and exhibits phase separation and crystallization during shelf life storage. Polymers stabilize the amorphous drug by antiplasticization, reducing molecular mobility, reducing chemical potential of drug, and increasing glass transition temperature in ASD. Here, drug-polymer miscibility is an important contributor to the physical stability of ASDs. The current Review discusses the basics of drug-polymer interactions with the major focus on the methods for the evaluation of solubility and miscibility of the drug in the polymer. Methods for the evaluation of drug-polymer solubility and miscibility have been classified as thermal, spectroscopic, microscopic, solid-liquid equilibrium-based, rheological, and computational methods. Thermal methods have been commonly used to determine the solubility of the drug in the polymer, while other methods provide qualitative information about drug-polymer miscibility. Despite advancements, the majority of these methods are still inadequate to provide the value of drug-polymer miscibility at room temperature. There is still a need for methods that can accurately determine drug-polymer miscibility at pharmaceutically relevant temperatures.
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Affiliation(s)
- Samarth D Thakore
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Junia Akhtar
- Department of Pharmaceutical Technology (Formulations), National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Ranjna Jain
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Amrit Paudel
- Research Center Pharmaceutical Engineering (RCPE) GmbH, Inffeldgasse 13, 8010 Graz, Austria.,Institute for Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Arvind K Bansal
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
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49
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Haghshenas H, Kaviani B, Firouzeh M, Tavakol H. Developing a variation of 3D-QSAR/MD method in drug design. J Comput Chem 2021; 42:917-929. [PMID: 33719136 DOI: 10.1002/jcc.26514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/22/2022]
Abstract
In continuation of the previous reports on a combination of 3D-quantitative structure-activity relationships (QSAR) with computational molecular dynamics (MD) studies, a new variation of 3D-QSAR/MD method has been employed for drug-design as an alternative or supplementary for the typical experimental methods. The presented method is more cost-effective and less time-consuming than the previous methods and avoids several restrictions of experimental methods, such as validity estimation, and predictability. For this purpose, seven inhibitors for bromodomain (BRD)-containing protein, as an important protein in the development of different types of cancer and responsible for oncogenic rearrangements, have been selected to study of their interactions by docking and MD simulations using molecular mechanics/generalized born surface area (MM/GBSA) method. To build the proposed model, a common variant of 3D-QSAR methods, comparative molecular field analysis has been employed using a dataset of 100 MD-extracted ligand conformations and their corresponding MM/GBSA BRD4-binding energies. The results showed excellent predictability of the generated model for both the training set and test groups. Finally, two new inhibitors were selected among total 4000 designed derivatives (generated through evolutionary techniques) using the proposed 3D-QSAR-MD model. The potentials of these inhibitors were assessed by MD simulations, which showed the higher inhibitory of these compounds than the previous inhibitors. Therefore, this method showed high potentials for acceleration of the procedure of drug design and a basis for joining researchers in computational biology and pharmaceutical sciences.
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Affiliation(s)
- Hamed Haghshenas
- Division of Biochemistry, Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Bita Kaviani
- Division of Genetics, Department of Biology, Faculty of Sciences, Islamic Azad University, Shahrekord, Iran
| | - Monireh Firouzeh
- Department of Nanobiotechnology, NourDanesh Institute of Higher Education, Isfahan, Iran
| | - Hossein Tavakol
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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50
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Alves KMA, Cardoso FJB, Honorio KM, de Molfetta FA. Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of <i>Leishmania mexicana</i>. Med Chem 2021; 16:784-795. [PMID: 31309897 DOI: 10.2174/1573406415666190712111139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. OBJECTIVE The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). METHODS A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. RESULTS Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. CONCLUSION The use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.
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Affiliation(s)
- Krisnna M A Alves
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo (USP), 03828-000, Sao Paulo, SP, Brazil.,Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fábio A de Molfetta
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
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